ATGC: WAVES

WAVES: a Web Application for Versatile Enhanced Bioinformatic Services

Marc Chakiachvili, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent Lefort

Bioinformatics, 35(1):140-142, 2018.

Preprint available on bioRXiv.

Summary

WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.

Availability and implementation

WAVES was developed with Django, a Python-based web framework. It was designed as a reusable web application. It is fully portable, as only a Python installation is required to run Django. It is licensed under GNU General Public License version 3.

WAVES components

WAVES-core

This is the main WAVES component.

GitHub repository: https://github.com/lirmm/waves-core
Documentation: http://waves-core.readthedocs.io
Installation guide: http://waves-core.readthedocs.io/en/latest/installation.html
Administration guide: http://waves-core.readthedocs.io/en/latest/user_doc/user_guide.html

Tutorial to create a 'Hello world' service: http://waves-core.readthedocs.io/en/latest/user_doc/howto/howto.html

Developer guide: http://waves-core.readthedocs.io/en/latest/dev_doc/dev_doc.html

Python code examples to interact with WAVES API: http://waves-core.readthedocs.io/en/latest/dev_doc/sample_code.html

WAVES-Galaxy

This is a WAVES adapter dedicated to Galaxy. Using the BioBlend python library, this adapter enables Galaxy services import into WAVES-core. WAVES-Galaxy automatically recognizes the tools available in a Galaxy instance.

GitHub repository: https://github.com/lirmm/waves-galaxy
Documentation: http://waves-galaxy-adaptors.readthedocs.io

WAVES-demo

This is a custom WAVES instance for demo purpose. It was created to show what could be done with Django functionalities to custom a WAVES installation.

GitHub repository: https://github.com/lirmm/waves-demo
Documentation: http://waves-demo.readthedocs.io
Demo: http://waves.demo.atgc-montpellier.fr

The changes that have been made are:

Use a different skin for the back-office interface.
Custom front-end interface.
Override the Service class.
Override the Authentication class.

Please note that anyone can login the back-office administration interface and create new services. Thus, for security reasons, we intentionally deactivated the jobs running procedure.

WAVES Singularity image

This is a Singularity container with a functional WAVES installation including two pre-configured services ('Hello world' and 'PhyML'). For testing purpose.

Singularity image: http://www.atgc-montpellier.fr/download/binaries/waves/wavestest.simg
Documentation: http://waves-core.readthedocs.io/en/latest/extensions.html#just-have-a-try

Contact

You may contact the WAVES support by e-mail : waves [at] lirmm.fr